The American surged three shots clear on Saturday ahead of the final round, and her concluding four-day total of 19-under 265 saw her finish four shots ahead of China’s Shanshan Feng.
Thompson set a new scoring record for the event with her four-round total and shot all four rounds in the 60s for the first time in her career. She also tops her previous best of 271 which she shot on three separate occasions, most recently at the 2013 Marathon Classic.
“Just a bunch of happiness right now, that's for sure,” said Thompson. “Words can't even describe the feeling I have right now.
“It's sort of like a rerun from Navistar, just having that feeling walking up to the 18th green, embracing the fans and just knowing you have the win under your belt.
“It means so much, especially to get it here in Malaysia.”
The win marks the teenager’s second win after claiming the 2011 Navistar LPGA Classic and is her first as a fully-fledged LPGA member.
Feng shot a 67 to pick up her second runner-up this season, a week after she won her second LPGA title in China.
Korea’s Lee Il-hee had to settle for joint third after leading the way for the first half of the event. Her disappointing final-day 73 left her on a total of 272 along with Norway’s Suzann Pettersen.